RetrogeneDB ID: retro_lcha_103

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH128287.1:94050..94351(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000003723
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKP1
• Ensembl ID: ENSLACG00000016599
• Aliases: None
• Description: None

Sequence

>retro_lcha_103
ATGCCTTCTATTAAACTGCAGAGTTCAGATGGGGAGATATTTGAAGTTGATGTGGAAATTGCAAAACAGTCTGTAACAAT
CAAGACTATGTTAGAAGATTTGGGCATGGATGATGAAGGCAATGAAGATCCTGTTCCACTGCTTAACGTTAATGCAGCTA
TTCTTAAAAAGGTGATACAGTGGTGTACACATCACAAGGATGACCCACCTCCCCCAGAGAATGATGAGAACAAGGAGAAA
AGGACAGATGATATTCCAGTGTGGGATCAGGAATTCCTCAAAAGTAGACCAAGGAACACTC

Alignment

ORF - retro_lcha_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.05 %
• Parental protein coverage: 61.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDESDEDPVPLPNVNAAILKKVIQWCTHHKDDPP
          MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDE..EDPVPL.NVNAAILKKVIQWCTHHKDDPP
Retrocopy MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGNEDPVPLLNVNAAILKKVIQWCTHHKDDPP

Parental  PPEDDENKEKRTDDIPVWDQEFL-KVDQGTL
          PPE.DENKEKRTDDIPVWDQEFL.KVDQGTL
Retrocopy PPENDENKEKRTDDIPVWDQEFL>KVDQGTL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	0.13 RPM	93.47 RPM
DRP000627_kidney	0.22 RPM	64.79 RPM
DRP000627_pectoral_fin	0.14 RPM	58.77 RPM
DRP000627_pelvic_fin	0.00 RPM	74.03 RPM
DRP000627_pharynx	0.19 RPM	142.11 RPM
DRP000627_tail_muscle	0.11 RPM	115.70 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_103 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017810	1 retrocopy	retro_amel_897,
Bos taurus	ENSBTAG00000025191	5 retrocopies	retro_btau_10, retro_btau_1062, retro_btau_1253, retro_btau_1444, retro_btau_1687,
Canis familiaris	ENSCAFG00000000994	5 retrocopies	retro_cfam_1613, retro_cfam_779, retro_cfam_813, retro_cfam_889, retro_cfam_965,
Callithrix jacchus	ENSCJAG00000013613	1 retrocopy	retro_cjac_112,
Cavia porcellus	ENSCPOG00000005164	8 retrocopies	retro_cpor_1038, retro_cpor_1133, retro_cpor_1345, retro_cpor_1446, retro_cpor_223, retro_cpor_243, retro_cpor_830, retro_cpor_832,
Echinops telfairi	ENSETEG00000007560	5 retrocopies	retro_etel_1730, retro_etel_515, retro_etel_758, retro_etel_762, retro_etel_811,
Felis catus	ENSFCAG00000031140	1 retrocopy	retro_fcat_653,
Gorilla gorilla	ENSGGOG00000022930	7 retrocopies	retro_ggor_1288, retro_ggor_1300, retro_ggor_2601, retro_ggor_2602, retro_ggor_2796, retro_ggor_2797, retro_ggor_778,
Latimeria chalumnae	ENSLACG00000016599	1 retrocopy	retro_lcha_103 ,
Loxodonta africana	ENSLAFG00000016832	1 retrocopy	retro_lafr_83,
Microcebus murinus	ENSMICG00000017588	3 retrocopies	retro_mmur_270, retro_mmur_803, retro_mmur_997,
Myotis lucifugus	ENSMLUG00000022919	13 retrocopies	retro_mluc_1455, retro_mluc_1738, retro_mluc_1895, retro_mluc_2009, retro_mluc_2260, retro_mluc_2261, retro_mluc_2520, retro_mluc_2527, retro_mluc_2557, retro_mluc_267, retro_mluc_383, retro_mluc_841, retro_mluc_944,
Macaca mulatta	ENSMMUG00000013046	7 retrocopies	retro_mmul_1171, retro_mmul_2082, retro_mmul_2091, retro_mmul_2508, retro_mmul_654, retro_mmul_795, retro_mmul_919,
Monodelphis domestica	ENSMODG00000014168	4 retrocopies	retro_mdom_1173, retro_mdom_155, retro_mdom_1648, retro_mdom_929,
Pongo abelii	ENSPPYG00000015783	7 retrocopies	retro_pabe_1915, retro_pabe_199, retro_pabe_2072, retro_pabe_2736, retro_pabe_2756, retro_pabe_626, retro_pabe_824,
Sorex araneus	ENSSARG00000008307	4 retrocopies	retro_sara_241, retro_sara_446, retro_sara_492, retro_sara_609,
Tupaia belangeri	ENSTBEG00000015544	15 retrocopies	retro_tbel_1227, retro_tbel_1279, retro_tbel_1327, retro_tbel_1758, retro_tbel_1787, retro_tbel_1903, retro_tbel_1905, retro_tbel_240, retro_tbel_3024, retro_tbel_3267, retro_tbel_3848, retro_tbel_405, retro_tbel_4095, retro_tbel_528, retro_tbel_711,